Atapuerca Sima de los Huesos remains were closer to the Neanderthals

Four and a half years ago I posted about a site in Spain, known as Atapuerca (What Science is all about), in it, I mentioned two studies that came to different conclusions: one stated that the human remains there resembled Neanderthals, the other that they were closer to the Denisovans than to the Neanderthals.

Today I read a paper that was published on Nov. 30, 2018 and which states that the teeth of remains from Atapuerca's Sima de los Huesos site shows that they had a close relationship to the later Neanderthal groups found in Europe.

The paywall protected abstract says:

"Enamel and dentin patterns have awakened a considerable interest in phylogenetic studies. However, almost nothing is known about the dental tissue proportions of European Pleistocene hominins, apart from Neanderthal populations. This study aims to assess the three-dimensional dental tissue proportions of permanent canines belonging to the extensive sample of hominin teeth at Sierra de Atapuerca (Spain) through the use of microtomographic techniques. Our results show that early and middle Pleistocene populations from Atapuerca exhibit large coronal and root dentine dimensions, as well as a thinly enamelled pattern, which has been traditionally considered an autapomorphic Neanderthal trait. Therefore, these results might support an early enamel thickness decrease which is already observed 800 kyr ago in Homo antecessor and maintained in later groups such as Sima de los Huesos and Neanderthal populations during the middle Pleistocene."

This is important because it shows that the Sima de los Huesos remains had a close relationship with the Homo neanderthalensis.

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Patagonian Monsters - Cryptozoology, Myths & legends in Patagonia Copyright 2009-2018 by Austin Whittall © 

An ancient American origin of hepatitis B virus

Human hepatitis B viruses (HBV) are found in human populations all around the world. They can be grouped into ten genotypes named A to J (each with their own subgenotypes).

The genotypes have a distinct geographical distribution as you can see in the map below (Source):

Hepatitis B virus global distribution of genotyhpes.

A can be found in Africa, Asia, Europe and North America. B in Eastern and Southeastern Asia. C in the same region and Central Asia. D in India and western Eurasia. E a recent apparition, found exclusively in Africa (not taken to the Americas with slave trading and probably 200 years old only - read more).

F and H are exclusive to South and Central America.

And here is the unusual thing, thse F and H genotypes are distinct from all the other ones: they branch from the phylogenetic tree as a separate and earlier branch as can be seen in the following trees from different authors:

HBV phylogenetic tree.Credits

HBV, another phylogenetic tree Note location of chimps and gorillas.Credits

HBV, a phylogenetic tree. See the branch of the woolly monkeys by the American F and H genotypes.Credits

So where did HBV originate? And here is the difficult question which cannot be answered by the usual Out of Africa theory (originated in African apes and passed on to humans there, spreading out of Africa as our ancestors migrated across the globe, reaching America last).

This time the evidence does not point towards a clear African origin. It seems that the oldest and most distant branch is rooted in America.

Margaret Littlejohn, Stephen Locarnini, and Lilly Yuen describe the five theories about HBV's origin and their shortcomings:

• New World origin (out of South America), and then reached the Old World after European discovery in 1492.
• Cospeciation: evolved in parallel in certain primate species over the past tens of millions of years.
• Coevolution as anatomically modern humans (AMH) migrated out of Africa. Caveat: "it does not fit with the close genetic relationships observed between primate and human HBV. Another inconsistency is that Native Americans predominantly have genotype F infections, whereas northeast-Asians, who are their closest relatives genetically, have genotypes B and C infections."
• Cross-species transmission, between human and nonhuman primates.
• Bat origin

The authors interestingly point out that "Given the arguments for and against each of these five theories, it is probable that HBV evolution cannot be explained by any single theory. The reality probably involves cospecies evolution within birds, rodents, and bats, followed by a series of cross-species transmission events to explain the close relationship between human and nonhuman primate HBVs observed today. Challenges for any unifying theory include the high level of genome divergence observed between HBV sequences of New World woolly monkeys and other nonhuman primates, w hich cannot be explained by the cross-species transmission theory, and also that HBV has only been detected in rodent species of the New World. If HBV coevolved with avian, rodent, and primate species, then why is it not found in all rodent and primate species? In addition, if HBV emerged out of Africa with AMH, then why are people from the New World, who are genetically most closely related to humans in the Far East, predominantly infected with HBV genotypes F and H rather than the genetically unrelated HBV genotypes B and C that are found in the Far East?"

As you can see, the American F variant and its presence in the New World woolly monkeys stand firmly against an Out of Africa origin.

Finally the paper mentions archaic hominins (Neanderthals, Denisovans and our admixing with them): "The influence of these various groups of archaic humans on the evolutionary history of HBV would be difficult to decipher. However, the possibility that human HBV may have originated, at least in part, from these archaic humans should not be discounted."

It is likely that it originated in the Americas in an Archaic (H. erectus) group and then moved into Asia and Africa (the most recent variant "E" is African after all!).

But Out of Africa is hard to beat. The author of a paper that studied HBV found in 7,000 year-old remains in Eurasia, is quoted here as follows:

"... it is still unclear how old HBV actually is. "It could be much older. It could even be coming out of Africa, which would explain why chimpanzees and gorillas fall together with the oldest HPV genomes" he adds. "That could be one explanation, but we also find it in the new world and new world monkeys and old world monkeys separated 60 million years ago, so it's very unlikely it's that old. There's lots of open question marks here."

But, he is mistaken, the gorillas and chimpanzees HBV does not align with the "oldest" groups (see second tree image further up), they lie closer to the more recent Eurasian variants..."

As usual, when an odd thing appears in the Americas which confronts the Out Of Africa theory, orthodox science finds it hard to explain them away and support the OOA theory.

Merry Christmas and Seasons Greetings to all our readers. And a Great 2019 for everyone!

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Patagonian Monsters - Cryptozoology, Myths & legends in Patagonia Copyright 2009-2018 by Austin Whittall © 

The "unsampled population" in America: archaic hominins?

I want to share an excellent article from "Ancient DNA Era", published on Nov. 27, 2018 by Alberto (Early human dispersals within the Americas – Moreno-Mayar et al. 2018).

In this article Alberto discusses a recent paper (Early human dispersals within the Americas, J. Victor Moreno-Mayar, Lasse Vinner, Peter de Barros Damgaard, Constanza de la Fuente et al, Science 08 Nov 2018 DOI: 10.1126/science.aav2621) which deals with "multiple independent, geographically uneven migrations, including one that provides clues of a Late Pleistocene Australasian genetic signal, and a later Mesoamerican-related expansion. These led to complex and dynamic population histories from North to South America."

Moreno-Mayar mentions:

"We sequenced 15 ancient human genomes spanning Alaska to Patagonia; six are ≥10,000 years old (up to ~18× coverage). All are most closely related to Native Americans (NA), including an Ancient Beringian individual, and two morphologically distinct "Paleoamericans." We find evidence of rapid dispersal and early diversification, including previously unknown groups, as people moved south. This resulted in multiple independent, geographically uneven migrations, including one that provides clues of a Late Pleistocene Australasian genetic signal, and a later Mesoamerican-related expansion."

Alberto focuses on the "previously unknown groups" and the "Australasian genetic signal" and he quotes the original paper:

"...further SFS-based modeling indicates that Mixe most likely carry gene flow from an unsampled outgroup […] Hereafter we refer to that outgroup as 'Unsampled population A' (UPopA), which is neither AB, NNA or SNA [Ancient Beringians, Northern Native Americans or Southern Native Americans], and which we infer split off from Native Americans ~24.7 ka, ranging from 30-22 ka (95% CI; this large range is a result of the analytical challenge of estimating divergence and admixture times in the absence of UPopA genome data).[…] Under a model with a pulse-like gene flow, we inferred a probability of ~11% gene flow from UPopA into Mixe ~8.7 ka (95% CI: 0.4-13.9 ka; the wide interval potentially reflects unmodeled continuous migration)"

Alberto then reasons as follows: (I quote him extensively below)

" When they say "unsampled", they mean unsampled. So no, we’re not talking about potentially "anyone", but quite specifically about a population that does not only seem to be an outgroup to NA, but also an outgroup to Eurasians.
If this is true, then who can be an outgroup to Eurasians? Basically there are 4 options:
– An African population (meaning a population that went Out of Africa after the main OoA event that gave birth to most Eurasians, and that somehow reached Central America some 9 kya). This one is the least likely, really.
– An early OoA population (meaning a population that went OoA before the main OoA event). We know from archaeology (and with some support from genetics) that such early events did occur but they hardly contributed to later Eurasian populations (maybe a tiny bit to some SE Asian/Australasian populations?). So this one would mean that such population made it to the Americas and survived somewhere around Central America until the second major wave arrived.
– Archaic hominins. Like Neandertals or Denisovans. A small admixture from such groups (on top of what other NA already have) would make the shared drift of Mixe with all other AMH be lower. So is it possible that some form of archaic hominin lived in America and survived until some 9 kya?
– A fourth option would be an early "generic" Eurasian population, something similar to Ust-Ishim samples from 45 kya, but not directly related to Ust-Ishim."

I favor option three "Archaic hominins" but Alberto believes option four is the most likely one.

Finally Alberto remarks: "Using qpGraph, this Australasian admixture is estimated to be around 3% in these samples (and modern Surui). How it got there (if it’s real, that it well could be) is unknown at this point, but it’s important to keep in mind that it was already present at least 10.4 kya, so it cannot be from any kind of Holocene migration of Australasians to South America. The possibility is that there was a small (?) population of Australasian origin at the arrival of the migrants of NE Siberian origin."

Skoglund already noticed the Australasian link in Native American DNA (See paper here and the other paper here) back in 2015.

In my book Monsters of Patagonia y point out the similarity between Australian and Patagonian native myths (read more), and conclude " Human remains discovered in Brazil show a very strong resemblance to modern South Pacific people, suggesting that America was first colonized by the generalized human (Homo sapiens) population that inhabited East Asia in the Late Pleistocene. These people arrived in America in very ancient times long before the Mongolid morphology of the forbearers of the Clovis had evolved."

We will have to wait for more evidence to learn about the unsampled population and the Australasian migrants.

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Patagonian Monsters - Cryptozoology, Myths & legends in Patagonia Copyright 2009-2018 by Austin Whittall © 

mtDNA can be inherited from both mother and father

A paper published in PNAS a few weeks ago -Nov. 26. 2018- (1), reports that mtDNA from both mother and father has been found in seventeen individuals.

This is a very important finding because until now, mtDNA in humans, was assumed to be inherited on a matrilineal basis: the mother's mtDNA was passed on to the nesxt generation.

This type of inheritance was the origin of the Out of Africa theory, by which all extant humans can trace their mtDNA to a woman living in Africa some 200,000 years ago.

And the splits between different human groups are all branches marked by different mutations of the original mtDNA lineage.

If the father's mtDNA can find its way into his offspring, this will alter the matrilineal inheritance and impact on the timescales used to estimate the origin of mankind.

This is what the paper says (abstract) -the rest is behind a paywall:

"Significance
The energy-producing organelle mitochondrion contains its own compact genome, which is separate from the nuclear genome. In nearly all mammals, this mitochondrial genome is inherited exclusively from the mother, and transmission of paternal mitochondria or mitochondrial DNA (mtDNA) has not been convincingly demonstrated in humans. In this paper, we have uncovered multiple instances of biparental inheritance of mtDNA spanning three unrelated multiple generation families, a result confirmed by independent sequencing across multiple unrelated laboratories with different methodologies. Surprisingly, this pattern of inheritance appears to be determined in an autosomal dominantlike manner. This paper profoundly alters a widespread belief about mitochondrial inheritance and potentially opens a novel field in mitochondrial medicine.
Abstract
Although there has been considerable debate about whether paternal mitochondrial DNA (mtDNA) transmission may coexist with maternal transmission of mtDNA, it is generally believed that mitochondria and mtDNA are exclusively maternally inherited in humans. Here, we identified three unrelated multigeneration families with a high level of mtDNA heteroplasmy (ranging from 24 to 76%) in a total of 17 individuals. Heteroplasmy of mtDNA was independently examined by high-depth whole mtDNA sequencing analysis in our research laboratory and in two Clinical Laboratory Improvement Amendments and College of American Pathologists-accredited laboratories using multiple approaches. A comprehensive exploration of mtDNA segregation in these families shows biparental mtDNA transmission with an autosomal dominantlike inheritance mode. Our results suggest that, although the central dogma of maternal inheritance of mtDNA remains valid, there are some exceptional cases where paternal mtDNA could be passed to the offspring. Elucidating the molecular mechanism for this unusual mode of inheritance will provide new insights into how mtDNA is passed on from parent to offspring and may even lead to the development of new avenues for the therapeutic treatment for pathogenic mtDNA transmission."

This had been reported back in 2002 (2) (see paper), this new study confirms the original finding.

Sources
(1) Biparental Inheritance of Mitochondrial DNA in Humans Shiyu Luo, C. Alexander Valencia, Jinglan Zhang, Ni-Chung Lee, Jesse Slone, Baoheng Gui, Xinjian Wang, Zhuo Li, Sarah Dell, Jenice Brown, Stella Maris hen, Yin-Hsiu Chien, Wuh-Liang Hwu, Pi-Chuan Fan, Lee-Jun Wong, Paldeep S. Atwal, Taosheng Huang Proceedings of the National Academy of Sciences Nov 2018, 201810946; DOI: 10.1073/pnas.1810946115

(2) Paternal inheritance of mitochondrial DNA, M Schwartz and J Vissing., N Engl J Med, Vol. 347, No. 8 pp. 576 August 22, 2002

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Patagonian Monsters - Cryptozoology, Myths & legends in Patagonia Copyright 2009-2014 by Austin Whittall ©